A federal appeals court Friday overturned a plea deal to resolve the Sept. 11, 2001, case with life sentences, a decision that could restart proceedings toward a lengthy death penalty trial at Guantánamo Bay.

The 2-1 decision was the latest upheaval for families awaiting a resolution in the long, agonizing case and likely means the conspiracy trial will not start soon. More appeals could come. Also, the previous military judge retired recently, and his replacement will need to read the voluminous record and decide threshold issues, including whether the confessions that prosecutors want to use were unlawfully obtained through torture.

A senior Pentagon official reached the deal in the summer of 2024 with Khalid Sheikh Mohammed, the man accused of being the mastermind of the plot, and two other defendants. Under the agreement, each would admit to his role in the plot to avert a capital trial.

Within days of the deal, then-Defense Secretary Lloyd Austin declared it void. But the judge in the case found that he was bound to the contract reached by the senior Pentagon official in charge of the war court, a retired Army lawyer whom Austin had appointed.

Friday, two judges on the U.S. Court of Appeals for the District of Columbia Circuit — Patricia A. Millett and Neomi J. Rao — found that Austin “indisputably had legal authority to withdraw from the agreements.”

The judges wrote that while prosecutors and defense lawyers presented the deal to the court in the summer of 2024, “no performance of promises had begun.”

Judge Robert L. Wilkins dissented. He said his colleagues should have deferred to the findings of two military courts that the contract was valid, and that the court should not have taken up the appeal. It took the three-judge panel more than five months to decide the case.

The settlement had stirred mixed reactions among the families of the nearly 3,000 people who were killed when hijackers crashed commercial airplanes in New York, Pennsylvania and the Pentagon.

Some argue that nothing short of a death sentence would bring resolution for the survivors, even if appeals over the defendants’ torture by the CIA ultimately avert an execution.

Others say that the only way to resolve the case is through a settlement in which the defendants give up most appeal rights. Without a conviction through a guilty plea, some relatives have said, the defendants could die at Guantánamo as essentially innocent men.

In the months after the deal was reached, the last judge, Col. Matthew N. McCall, heard testimony about the conditions and abusive treatment of a fourth defendant in the case, Ammar al-Baluchi, and threw out his 2007 confessions to FBI agents as obtained through his torture in CIA custody from 2003 to 2006.

McCall ruled that a fifth defendant, Ramzi Binalshibh, was mentally unfit to face trial, and severed him from the case. His lawyer blamed his post-traumatic stress disorder with psychotic features on his torture by the CIA.

Mohammed, 61, and his two codefendants will have to decide whether to appeal the ruling to a full panel of the court of appeals, or seek review by the U.S. Supreme Court in the next session.

The two other defendants are Walid bin Attash, who is accused of helping to train two of the 19 hijackers in the plot, and Mustafa al-Hawsawi, who is accused of helping some of the hijackers with finances.

If the case is returned to trial, the next judge would likely need to restart hearings on whether the confessions of those three men to the CIA in 2007 and 2008 were also unlawfully obtained. Mohammed was waterboarded, rectally abused in a manner that his lawyers describe as rape, sleep deprived and subjected to other “enhanced interrogation techniques” by the CIA after he was captured in Pakistan in March 2003.

Based on the ruling, Defense Secretary Pete Hegseth now has the authority to negotiate and, in the panel’s words, “superintend the disposition of charges in these cases.”

During a visit to Guantánamo in February, Hegseth said he agreed with Austin that Mohammed “deserves the death penalty.”

He added: “And I hope he finds it soon, through that system.”

An eventual trial could last more than a year and require weeks or months of selection of a panel of military officers, according to people associated with the process. Although the further the trial recedes from the attacks themselves, the less likely members of the jury pool would have direct connections to the events of 9/11.